The Modified format was introduced in 2001, when tournaments in the 2001-2002 season were played in a format that only allowed cards from the Team Rocket set on up to Neo Genesis (minus Sneasel from Neo Genesis), at that point in time the most recent English expansion, plus any expansions released afterward on the day of their release as well as many of the most recent promotional cards. The format had been altered every year by rotating older sets and promo cards out of the format, keeping the pool of cards usable in a tournament season roughly that of the previous year; however, the 2009-10 tournament season did not feature a rotation, and the rotation for the 2010-11 season rotated out only four sets, keeping roughly two years' worth of cards in the pool. The 2010-2011 season later featured a mid-season rotation to any cards from the HeartGold & SoulSilver set or later.

If a card in a Modified-legal expansion is a reprint of an older card, all prints of the card can be played in a Modified-legal deck (i.e. Base SetPotion, whose most recent reprint is in Black & White), provided that the card has been printed with artwork corresponding to a set that has been released in English. However, some cards are different in wording between older prints and newer prints (i.e. Charizard from the Base Set compared to its Stormfront iteration); those cards require a reference outside the deck in order to use the older prints in a Modified-legal deck, such reference is either a print of the card that doesn't require a reference or a printout of the card's entry from the official Card-Dex.

Prior to the 2009-10 tournament season, foreign-language prints of cards could also be played without limit, as long as a local-language reference outside the deck was provided in a similar manner to those with vastly different wording. It had been announced that, starting with the 2009-10 season, however, official events will require players to play with cards printed in English as well as any other language considered a local language by Pokémon Organized Play (i.e. players in the United States would be restricted to English cards only, whereas players in Canada can also use cards in French and players in Mexico can also use cards in Spanish). This has caused an outcry in the TCG community, as many American players have invested heavily in Japanese cards to use in tournaments due to the price discrepancy between Japanese and English cards. As a result, a late rule draft modified the rules for the 2009-10 tournament season that allowed up to 10% of a player's deck (six cards in a normal deck) to consist of foreign-language cards, and those cards must come from sets corresponding to the English Supreme Victors set and all sets before that; many see this decision as allowing a transitional period to eventually phase out the usage of foreign cards for the 2010-11 tournament season.